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[![pipeline status](https://git-r3lab.uni.lu/piotr.gawron/big-bed-generator/badges/master/pipeline.svg)](https://git-r3lab.uni.lu/piotr.gawron/big-bed-generator/commits/master)

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# Introduction
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This project aim is to provide simple tool that creates [BigBed](https://genome.ucsc.edu/goldenpath/help/bigBed.html) file from gene definition downloadable from [UCSC](http://hgdownload.cse.ucsc.edu/downloads.html). The script is designed to be run on linux and uses heavily tools provided by UCSC: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

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# Usage
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Download definition of genes. For instance to download refGene definition for human hg38 reference genome execute:

```
curl http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz -o refGene.txt.gz
```

Now you can call the script providing as an input file with genes and identifier of the reference genome:

```
python3 generate.py refGene-19.txt.gz hg19
```

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This should generate file called `refGene-19.bb`